test.data.3comp: Simulated three-component mixed cell line test data

In wwylab/DeMixT: Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

Simulated three-component mixed cell line test data

Description

A list of simulated three-component mixed cell line test data used in DeMixT function. Expression data with 700 genes and 20 samples are simulated, where 675 genes' MuN1 is close to MuN2.

Usage

test.data.3comp

Format

An object of class list of length 6.

Value

A list with 6 elements (3 more elements when output.more.info = TRUE), which are

pi	A matrix of estimated proportion. First row and second row corresponds to the proportion estimate for the known components and unkown component respectively for two or three component settings. Each column corresponds to one sample.
Mu	Simulated Mu of log2-normal distribution for both known (MuN1, MuN2) and unknown component (MuT).
Sigma	Simulated Sigma of log2-normal distribution for both known (SigmaN1, SigmaN2) and unknown component (SigmaT).
data.Y	A SummarizedExperiment object of simulated expression data from mixed tumor samples. It is a G by My matrix where G is the number of genes and My is the number of mixed samples. Samples with the same tissue type should be placed together in columns.
data.N1	A SummarizedExperiment object of simulated expression data from reference component 1 (e.g., normal). It is a G by M1 matrix where G is the number of genes and M1 is the number of samples for component 1.
data.N2	A SummarizedExperiment object of expression data from additional reference samples. It is a G by M2 matrix where G is the number of genes and M2 is the number of samples for component 2.
True.data.T	A SummarizedExperiment object of simulated tumor expression data. It is a G by My matrix, where G is the number of genes and My is the number of mixed samples.This is shown only when output.more.info = TRUE.
True.data.N1	A SummarizedExperiment object of simulated true expression data for reference component 1 (e.g., stroma). It is a G by M1 matrix where G is the number of genes and M1 is the number of samples for component 1. This is shown only when output.more.info = TRUE.
True.data.N2	A SummarizedExperiment object of simulated true expression data for reference component 2 (e.g., immue). It is a G by M2 matrix where G is the number of genes and M2 is the number of samples for component 2. This is shown only when output.more.info = TRUE.

wwylab/DeMixT documentation built on July 17, 2024, 9:14 p.m.